Align NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized)
to candidate WP_086511010.1 BZY95_RS16615 carbohydrate ABC transporter permease
Query= TCDB::Q8RJU8 (307 letters) >NCBI__GCF_002151265.1:WP_086511010.1 Length = 275 Score = 159 bits (401), Expect = 9e-44 Identities = 88/264 (33%), Positives = 148/264 (56%), Gaps = 4/264 (1%) Query: 45 ILVLWAFMVVLPLLWAVMTSFKDDASIFGSPWSLPDKLHFDNWSRAWTEAHMGDYFLNTV 104 +L+L A +V+ PLL + FK +A + +P LPD + N+ + + + Y N+ Sbjct: 14 VLILVASLVIGPLLASFFGGFKTNAELRTNPLWLPDAWNPQNYVAIFLDGNFWRYMGNSF 73 Query: 105 LVVGGSLIGTLVLGSMAAYVLARFDFPGNRFIYYLFIGGMSFPIMLALVPLFYVVNNMGL 164 + +++ TLV+G+ AAYV ++ F G+R I+ + G+ FP A++PLF V ++GL Sbjct: 74 FISSMTVLLTLVVGAAAAYVFSQIRFFGSRMIHSYLLLGLMFPFAAAILPLFIKVRDLGL 133 Query: 165 LNTLHGLILVYIAYSLPFTVFFLTAFFRTLPSSVAEAAFVDGASHTRTFFQIMLPMAKPG 224 L+T +IL A+ L + AFF LP + EAA+VDG S+ R F+ LP++ P Sbjct: 134 LDTYWAVILPQTAFGLSLAILLFKAFFDQLPKELFEAAYVDGCSYLRFFWSFTLPLSTPI 193 Query: 225 LISVGIFNFLGQWNQYMLP-TVLNTDPDKRVLTQGLVQLAVSQGYKGDWSGLFAGLVMAM 283 L +VG+F F+ WN ++LP VLN D+ + T L + Y W+ + A + + + Sbjct: 194 LATVGVFVFVQSWNNFLLPLVVLN---DRSIYTWPLGMMQFQGEYLTQWNMILAFVTLTI 250 Query: 284 LPVLAAYIIFQRQVVQGLTAGALK 307 P + ++ Q+ +V GLT G++K Sbjct: 251 TPAVIFFLAAQKYIVAGLTGGSVK 274 Lambda K H 0.326 0.141 0.440 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 301 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 307 Length of database: 275 Length adjustment: 26 Effective length of query: 281 Effective length of database: 249 Effective search space: 69969 Effective search space used: 69969 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory